"The secretary-general strongly regrets the decision of the Sri Lankan government to expel Mr.
James Elder," Ban's office said in a statement.
The UN chief "expresses his full confidence in the work of the United Nations in Sri Lanka, which includes making public statements when necessary in an effort to save lives and prevent grave humanitarian problems.
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Ban added that the international body was "working impartially to assist the people of Sri Lanka, and the government should be supporting and cooperating with its efforts."
The UN secretary-general, who visited the island in May, would take up the matter directly with Sri Lankan President Mahinda Rajapaksa, the statement added.
Elder, communications chief for UNICEF in Sri Lanka, was told on Sunday to leave the country within two weeks.
He has worked in Sri Lanka since July 2008 and his residency visa was valid until 2010.
Foreign Secretary Palitha Kohona on Sunday accused Elder of being biased towards the Liberation Tiger